Between-sample variability from 16S rRna-gene sequencing data.
Clustering by timepoint (PCA):
Clustering by treatment (PCA): by timepoints
Before_oil
## Saving 7 x 5 in image
After_oil
## Saving 7 x 5 in image
## Warning in metaMDS(matxTP, k = 3): stress is (nearly) zero: you may have
## insufficient data
NMDS1 vs NMDS2
## Warning in metaMDS(matx, k = 3): stress is (nearly) zero: you may have
## insufficient data
Clustering by type (MDS): NMDS1 vs NMDS3
Clustering by type (MDS): NMDS2 vs NMDS3
## Warning in metaMDS(matx): stress is (nearly) zero: you may have insufficient
## data
Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.
Below the ANOVA table from the model:
\[ X = \mu + treatment + timepoint + treatment*type + e \]
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| treatment | 1 | 0.1439951 | 0.1439951 | 1.313483 | 0.0417820 | 0.128 |
| timepoint | 1 | 0.1231220 | 0.1231220 | 1.123084 | 0.0357254 | 0.254 |
| treatment_by_timepoint | 29 | 3.1792253 | 0.1096285 | NA | 0.9224926 | NA |
| residuals | 31 | 3.4463424 | NA | NA | 1.0000000 | NA |
## Run 0 stress 0.0001263224
## Run 1 stress 9.891639e-05
## ... New best solution
## ... Procrustes: rmse 0.00018548 max resid 0.0006609065
## ... Similar to previous best
## Run 2 stress 9.998749e-05
## ... Procrustes: rmse 9.377306e-05 max resid 0.0002382569
## ... Similar to previous best
## Run 3 stress 9.846708e-05
## ... New best solution
## ... Procrustes: rmse 0.0001415423 max resid 0.000499575
## ... Similar to previous best
## Run 4 stress 9.953504e-05
## ... Procrustes: rmse 0.0001596566 max resid 0.0005405929
## ... Similar to previous best
## Run 5 stress 9.852399e-05
## ... Procrustes: rmse 3.578719e-05 max resid 0.0001329834
## ... Similar to previous best
## Run 6 stress 9.996312e-05
## ... Procrustes: rmse 1.900173e-05 max resid 7.960467e-05
## ... Similar to previous best
## Run 7 stress 9.904341e-05
## ... Procrustes: rmse 1.954365e-05 max resid 9.126139e-05
## ... Similar to previous best
## Run 8 stress 9.794829e-05
## ... New best solution
## ... Procrustes: rmse 0.0001054845 max resid 0.0002977778
## ... Similar to previous best
## Run 9 stress 9.944269e-05
## ... Procrustes: rmse 0.0001083153 max resid 0.0003207916
## ... Similar to previous best
## Run 10 stress 9.844764e-05
## ... Procrustes: rmse 0.0001197334 max resid 0.0004473062
## ... Similar to previous best
## Run 11 stress 9.744944e-05
## ... New best solution
## ... Procrustes: rmse 7.03499e-05 max resid 0.0003191853
## ... Similar to previous best
## Run 12 stress 9.496812e-05
## ... New best solution
## ... Procrustes: rmse 0.0001236837 max resid 0.0005617767
## ... Similar to previous best
## Run 13 stress 9.841598e-05
## ... Procrustes: rmse 0.0001488383 max resid 0.000560692
## ... Similar to previous best
## Run 14 stress 9.785192e-05
## ... Procrustes: rmse 0.0001435198 max resid 0.000556119
## ... Similar to previous best
## Run 15 stress 9.809965e-05
## ... Procrustes: rmse 0.0001370057 max resid 0.0004814745
## ... Similar to previous best
## Run 16 stress 0.0001599563
## ... Procrustes: rmse 0.0002432481 max resid 0.0008920106
## ... Similar to previous best
## Run 17 stress 9.675082e-05
## ... Procrustes: rmse 0.0001120027 max resid 0.0003662987
## ... Similar to previous best
## Run 18 stress 9.677233e-05
## ... Procrustes: rmse 0.0001646299 max resid 0.0006686248
## ... Similar to previous best
## Run 19 stress 9.428191e-05
## ... New best solution
## ... Procrustes: rmse 0.0001440906 max resid 0.0004131426
## ... Similar to previous best
## Run 20 stress 9.992988e-05
## ... Procrustes: rmse 7.914129e-05 max resid 0.0002852179
## ... Similar to previous best
## *** Solution reached